Check the first post of ixtab's thread, but, basically, to nest collections, the [X-->] & [<--X] button is your new best friend
Originally Posted by ixtab
- The Import function will never remove collections; it will only update existing collections, or create new ones (visible in home by default). In particular, this means that after deleting collections from Calibre, you may also have to manually delete these collections from the Kindle.
- Calibre Synchronization will never change the collection hierarchy, or the visibility of existing items. This applies to both import and export.